FMO DATABASE

FMODB ID: 89M8Y

Calculation Name: 3EJ9-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EJ9

Chain ID: B

ChEMBL ID:

UniProt ID: Q9EV84

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	59
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-272924.035948
FMO2-HF: Nuclear repulsion	250312.240062
FMO2-HF: Total energy	-22611.795886
FMO2-MP2: Total energy	-22677.44757

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(B:1:PRO)

Summations of interaction energy for fragment #1(B:1:PRO)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-9.436	-7.273	19.514	-9.495	-12.18	-0.049

Interaction energy analysis for fragmet #1(B:1:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.032

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

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Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	B	3	ILE	0	0.000	0.003	3.108	-0.629	1.471	0.074	-0.799	-1.375	0.000
4	B	4	GLU	-1	-0.881	-0.943	5.497	-0.314	-0.314	0.000	0.000	0.000	0.000
5	B	5	CYS	0	-0.076	-0.045	9.269	0.079	0.079	0.000	0.000	0.000	0.000
6	B	6	HIS	0	0.064	0.055	11.695	-0.003	-0.003	0.000	0.000	0.000	0.000
7	B	7	ILE	0	-0.019	-0.015	15.174	0.018	0.018	0.000	0.000	0.000	0.000
8	B	8	ALA	0	0.078	0.042	17.746	0.005	0.005	0.000	0.000	0.000	0.000
9	B	9	THR	0	-0.018	-0.015	21.064	-0.017	-0.017	0.000	0.000	0.000	0.000
10	B	10	GLY	0	0.037	0.016	23.016	0.009	0.009	0.000	0.000	0.000	0.000
11	B	11	LEU	0	-0.020	0.000	18.614	0.001	0.001	0.000	0.000	0.000	0.000
12	B	12	SER	0	0.037	0.019	22.502	-0.006	-0.006	0.000	0.000	0.000	0.000
13	B	13	VAL	0	0.063	0.007	20.788	-0.018	-0.018	0.000	0.000	0.000	0.000
14	B	14	ALA	0	0.029	0.015	19.878	-0.027	-0.027	0.000	0.000	0.000	0.000
15	B	15	ARG	1	0.932	0.967	17.212	0.224	0.224	0.000	0.000	0.000	0.000
16	B	16	LYS	1	0.903	0.944	16.902	0.206	0.206	0.000	0.000	0.000	0.000
17	B	17	GLN	0	0.013	0.004	15.271	-0.047	-0.047	0.000	0.000	0.000	0.000
18	B	18	GLN	0	-0.051	-0.010	15.036	-0.036	-0.036	0.000	0.000	0.000	0.000
19	B	19	LEU	0	-0.009	0.005	12.954	-0.018	-0.018	0.000	0.000	0.000	0.000
20	B	20	ILE	0	0.039	0.019	9.983	-0.032	-0.032	0.000	0.000	0.000	0.000
21	B	21	ARG	1	0.905	0.939	10.172	0.255	0.255	0.000	0.000	0.000	0.000
22	B	22	ASP	-1	-0.831	-0.921	11.380	-0.404	-0.404	0.000	0.000	0.000	0.000
23	B	23	VAL	0	-0.013	0.000	6.478	0.025	0.025	0.000	0.000	0.000	0.000
24	B	24	ILE	0	-0.010	-0.006	6.636	-0.074	-0.074	0.000	0.000	0.000	0.000
25	B	25	ASP	-1	-0.901	-0.952	7.306	-0.431	-0.431	0.000	0.000	0.000	0.000
26	B	26	VAL	0	0.013	0.001	8.720	0.053	0.053	0.000	0.000	0.000	0.000
27	B	27	THR	0	-0.005	0.008	2.664	-0.480	0.089	0.438	-0.191	-0.816	-0.001
28	B	28	ASN	0	-0.075	-0.046	5.539	0.258	0.258	0.000	0.000	0.000	0.000
29	B	29	LYS	1	0.909	0.957	6.831	0.377	0.377	0.000	0.000	0.000	0.000
30	B	30	SER	0	-0.098	-0.051	7.532	0.105	0.105	0.000	0.000	0.000	0.000
31	B	31	ILE	0	-0.024	-0.021	2.417	-0.026	-0.199	1.477	-0.214	-1.089	0.000
32	B	32	GLY	0	0.010	0.016	6.817	0.062	0.062	0.000	0.000	0.000	0.000
33	B	33	SER	0	-0.030	-0.013	2.091	-1.543	-0.394	1.639	-1.030	-1.758	-0.001
34	B	34	ASP	-1	-0.815	-0.906	4.691	-0.706	-0.707	-0.001	-0.007	0.009	0.000
35	B	35	PRO	0	0.047	-0.005	5.003	-0.648	-0.592	-0.001	-0.001	-0.053	0.000
36	B	36	LYS	1	0.908	0.961	6.538	0.048	0.048	0.000	0.000	0.000	0.000
37	B	37	ILE	0	-0.039	-0.003	2.524	-1.124	0.299	0.476	-0.588	-1.311	-0.001
38	B	38	ILE	0	-0.054	-0.007	1.809	-6.627	-10.530	15.405	-6.487	-5.015	-0.046
39	B	39	ASN	0	-0.044	-0.012	3.287	2.345	3.339	0.008	-0.159	-0.843	0.000
40	B	40	VAL	0	0.003	-0.004	4.953	-0.327	-0.378	-0.001	-0.019	0.071	0.000
41	B	41	LEU	0	-0.005	0.011	7.458	0.200	0.200	0.000	0.000	0.000	0.000
42	B	42	LEU	0	-0.036	-0.018	10.571	0.037	0.037	0.000	0.000	0.000	0.000
43	B	43	VAL	0	0.018	0.007	13.217	0.028	0.028	0.000	0.000	0.000	0.000
44	B	44	GLU	-1	-0.876	-0.935	16.088	-0.206	-0.206	0.000	0.000	0.000	0.000
45	B	45	HIS	0	-0.022	-0.025	17.258	0.027	0.027	0.000	0.000	0.000	0.000
46	B	46	ALA	0	-0.008	-0.013	21.923	-0.002	-0.002	0.000	0.000	0.000	0.000
47	B	47	GLU	-1	-0.871	-0.960	24.617	-0.092	-0.092	0.000	0.000	0.000	0.000
48	B	48	ALA	0	-0.029	-0.013	25.765	0.005	0.005	0.000	0.000	0.000	0.000
49	B	49	ASN	0	-0.062	-0.022	24.317	0.013	0.013	0.000	0.000	0.000	0.000
50	B	50	MET	0	-0.038	0.000	20.394	-0.005	-0.005	0.000	0.000	0.000	0.000
51	B	51	SER	0	-0.003	-0.004	22.541	0.005	0.005	0.000	0.000	0.000	0.000
52	B	52	ILE	0	0.018	0.008	18.826	0.005	0.005	0.000	0.000	0.000	0.000
53	B	53	SER	0	-0.062	-0.057	22.221	0.002	0.002	0.000	0.000	0.000	0.000
54	B	54	GLY	0	0.031	0.015	24.087	0.001	0.001	0.000	0.000	0.000	0.000
55	B	55	ARG	1	0.943	0.989	23.762	0.035	0.035	0.000	0.000	0.000	0.000
56	B	56	ILE	0	0.061	0.048	27.140	-0.004	-0.004	0.000	0.000	0.000	0.000
57	B	57	HIS	0	0.045	0.014	27.746	0.000	0.000	0.000	0.000	0.000	0.000
58	B	58	GLY	0	-0.028	-0.012	29.628	0.002	0.002	0.000	0.000	0.000	0.000
59	B	59	GLU	-1	-1.009	-0.992	32.640	-0.020	-0.020	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:1:PRO)